Literature DB >> 22723345

Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR.

Michael J Knight1, Andrew J Pell, Ivano Bertini, Isabella C Felli, Leonardo Gonnelli, Roberta Pierattelli, Torsten Herrmann, Lyndon Emsley, Guido Pintacuda.   

Abstract

We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with (1)H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of (15)N and (13)C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu(+) (diamagnetic) or Cu(2+) (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to (1)H-(1)H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable.

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Year:  2012        PMID: 22723345      PMCID: PMC3396464          DOI: 10.1073/pnas.1204515109

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  45 in total

1.  Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Authors:  Torsten Herrmann; Peter Güntert; Kurt Wüthrich
Journal:  J Mol Biol       Date:  2002-05-24       Impact factor: 5.469

2.  Sensitive high resolution inverse detection NMR spectroscopy of proteins in the solid state.

Authors:  Eric K Paulson; Corey R Morcombe; Vadim Gaponenko; Barbara Dancheck; R Andrew Byrd; Kurt W Zilm
Journal:  J Am Chem Soc       Date:  2003-12-24       Impact factor: 15.419

3.  Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS.

Authors:  Torsten Herrmann; Peter Güntert; Kurt Wüthrich
Journal:  J Biomol NMR       Date:  2002-11       Impact factor: 2.835

4.  Atomic structures of wild-type and thermostable mutant recombinant human Cu,Zn superoxide dismutase.

Authors:  H E Parge; R A Hallewell; J A Tainer
Journal:  Proc Natl Acad Sci U S A       Date:  1992-07-01       Impact factor: 11.205

5.  Superoxide dismutase. An enzymic function for erythrocuprein (hemocuprein).

Authors:  J M McCord; I Fridovich
Journal:  J Biol Chem       Date:  1969-11-25       Impact factor: 5.157

6.  The three-dimensional structure in solution of the paramagnetic high-potential iron-sulfur protein I from Ectothiorhodospira halophila through nuclear magnetic resonance.

Authors:  L Banci; I Bertini; L D Eltis; I C Felli; D H Kastrau; C Luchinat; M Piccioli; R Pierattelli; M Smith
Journal:  Eur J Biochem       Date:  1994-10-15

7.  Backbone dynamics of human Cu,Zn superoxide dismutase and of its monomeric F50E/G51E/E133Q mutant: the influence of dimerization on mobility and function.

Authors:  L Banci; I Bertini; F Cramaro; R Del Conte; A Rosato; M S Viezzoli
Journal:  Biochemistry       Date:  2000-08-08       Impact factor: 3.162

8.  The structure of holo and metal-deficient wild-type human Cu, Zn superoxide dismutase and its relevance to familial amyotrophic lateral sclerosis.

Authors:  Richard W Strange; Svetlana Antonyuk; Michael A Hough; Peter A Doucette; Jorge A Rodriguez; P John Hart; Lawrence J Hayward; Joan S Valentine; S Samar Hasnain
Journal:  J Mol Biol       Date:  2003-05-09       Impact factor: 5.469

9.  High-sensitivity observation of dipolar exchange and NOEs between exchangeable protons in proteins by 3D solid-state NMR spectroscopy.

Authors:  Eric K Paulson; Corey R Morcombe; Vadim Gaponenko; Barbara Dancheck; R Andrew Byrd; Kurt W Zilm
Journal:  J Am Chem Soc       Date:  2003-11-26       Impact factor: 15.419

10.  Protein fold determined by paramagnetic magic-angle spinning solid-state NMR spectroscopy.

Authors:  Ishita Sengupta; Philippe S Nadaud; Jonathan J Helmus; Charles D Schwieters; Christopher P Jaroniec
Journal:  Nat Chem       Date:  2012-03-18       Impact factor: 24.427

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  62 in total

1.  Asynchronous through-bond homonuclear isotropic mixing: application to carbon-carbon transfer in perdeuterated proteins under MAS.

Authors:  Natalia Kulminskaya; Suresh Kumar Vasa; Karin Giller; Stefan Becker; Rasmus Linser
Journal:  J Biomol NMR       Date:  2015-08-30       Impact factor: 2.835

2.  Spectral editing at ultra-fast magic-angle-spinning in solid-state NMR: facilitating protein sequential signal assignment by HIGHLIGHT approach.

Authors:  Songlin Wang; Isamu Matsuda; Fei Long; Yoshitaka Ishii
Journal:  J Biomol NMR       Date:  2016-01-19       Impact factor: 2.835

3.  Sensitivity and resolution of proton detected spectra of a deuterated protein at 40 and 60 kHz magic-angle-spinning.

Authors:  Andrew J Nieuwkoop; W Trent Franks; Kristina Rehbein; Anne Diehl; Ümit Akbey; Frank Engelke; Lyndon Emsley; Guido Pintacuda; Hartmut Oschkinat
Journal:  J Biomol NMR       Date:  2015-02-08       Impact factor: 2.835

4.  Out-and-back 13C-13C scalar transfers in protein resonance assignment by proton-detected solid-state NMR under ultra-fast MAS.

Authors:  Emeline Barbet-Massin; Andrew J Pell; Kristaps Jaudzems; W Trent Franks; Joren S Retel; Svetlana Kotelovica; Inara Akopjana; Kaspars Tars; Lyndon Emsley; Hartmut Oschkinat; Anne Lesage; Guido Pintacuda
Journal:  J Biomol NMR       Date:  2013-06-29       Impact factor: 2.835

5.  Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins.

Authors:  Marco Fragai; Claudio Luchinat; Giacomo Parigi; Enrico Ravera
Journal:  J Biomol NMR       Date:  2013-08-30       Impact factor: 2.835

6.  SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR.

Authors:  Lucio Ferella; Claudio Luchinat; Enrico Ravera; Antonio Rosato
Journal:  J Biomol NMR       Date:  2013-11-17       Impact factor: 2.835

7.  Capturing a reactive state of amyloid aggregates: NMR-based characterization of copper-bound Alzheimer disease amyloid β-fibrils in a redox cycle.

Authors:  Sudhakar Parthasarathy; Brian Yoo; Dan McElheny; William Tay; Yoshitaka Ishii
Journal:  J Biol Chem       Date:  2014-02-12       Impact factor: 5.157

8.  Zinc-binding structure of a catalytic amyloid from solid-state NMR.

Authors:  Myungwoon Lee; Tuo Wang; Olga V Makhlynets; Yibing Wu; Nicholas F Polizzi; Haifan Wu; Pallavi M Gosavi; Jan Stöhr; Ivan V Korendovych; William F DeGrado; Mei Hong
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-31       Impact factor: 11.205

9.  Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.

Authors:  Matthew D Shannon; Theint Theint; Dwaipayan Mukhopadhyay; Krystyna Surewicz; Witold K Surewicz; Dominique Marion; Paul Schanda; Christopher P Jaroniec
Journal:  Chemphyschem       Date:  2018-11-07       Impact factor: 3.102

Review 10.  Magic angle spinning NMR of viruses.

Authors:  Caitlin M Quinn; Manman Lu; Christopher L Suiter; Guangjin Hou; Huilan Zhang; Tatyana Polenova
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2015-02-16       Impact factor: 9.795

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